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The ship's function was mostly to run errands for the Federation when needed. From 2374 to 2376, the Manila was for the most part commanded by its First Officer, CommanderAvery - due to Captain Cid working more closely with Admiral's Theseus and Cloud aboard Starbase 55. In 2376, Avery was lost to the Gordarions, and Cid realized his neglect for his ship. From then on, he took a more active role as commanding officer.

Due to Theseus' and Cid's direct involvement with the Phoenix-X, some of the crew of the Manila may have been aware of the Phoenix-X's collaboration with Section 31. ("Experimentalism")